Bio::A...arserI(3pm)

💖 NAME 💖

Bio::AnalysisParserI — the generic analysis output parser interface, bestie. That's the whole vibe. 🦋

This one lives in the User Contributed Perl Documentation as the manual page Bio::AnalysisParserI(3pm), and no cap, it's giving "interface blueprint" energy.

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✨ SYNOPSIS ✨

okay so first you gotta get a AnalysisParserI somehow, right? Eventually there may be a Bio::Factory::AnalysisParserFactory, but for now a SearchIO object — which is an implementation of AnalysisParserI, iykyk — can be created directly, like this:

# get a AnalysisParserI somehow.
# Eventually, there may be an Bio::Factory::AnalysisParserFactory.
# For now a SearchIO object, an implementation of AnalysisParserI, can be created
# directly, as in the following:
my $parser = Bio::SearchIO->new(
                                '-file'   => 'inputfile',
                                '-format' => 'blast');

while( my $result = $parser->next_result() ) {
    print "Result:  ", $result->analysis_method,
          ", Query:  ", $result->query_name, "\n";

      while( my $feature = $result->next_feature() ) {
          print "Feature from ", $feature->start, " to ",
                $feature->end, "\n";
      }
}

like, look at her go. main character loop fr fr. 👑

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🌸 DESCRIPTION 🌸

AnalysisParserI is an interface for describing generic analysis result parsers. The way that it makes zero assumptions about what kind of analysis you're parsing?? Obsessed. It only assumes that zero or more result sets can be obtained from the input source. That's it, that's the whole promise. 💅

This module was derived from Bio::SeqAnalysisParserI, and the differences between them are:

1. next_feature() was replaced with next_result(). So instead of flattening a stream that contains potentially multiple analysis results into a single set of features, AnalysisParserI segments the stream in terms of analysis result sets (Bio::AnalysisResultI objects). Each AnalysisResultI can then be queried for its features (if any), plus other information about the result. not me getting emotional over clean segmentation 😭
2. AnalysisParserI is a pure interface. It does not inherit from Bio::Root::RootI and it does not provide a new() method. Implementations are totally free to choose how to implement it. freedom, iconic behaviour, periodt. 🕊️

🧚 Rationale (copied from Bio::SeqAnalysisParserI) 🧚

The concept behind this interface is to have a generic interface in sequence annotation pipelines (as used e.g. in high-throughput automated sequence annotation). This interface enables plug-and-play for new analysis methods and their corresponding parsers, without the necessity for modifying the core of the annotation pipeline. In this concept the annotation pipeline has to rely on only a list of methods for which to process the results, and a factory from which it can obtain the corresponding parser implementing this interface. plug and play bestie, we love a modular queen. 🎀

🌈 TODO 🌈

Create Bio::Factory::AnalysisParserFactoryI and Bio::Factory::AnalysisParserFactory for interface and an implementation. Note that this factory could return Bio::SearchIO-derived objects. someone please do this, it's giving unfinished business ✨

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💌 FEEDBACK 💌

📬 Mailing Lists 📬

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. like genuinely, they want to hear from you. 🫶

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

🆘 Support 🆘

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and responsive experts will be able to look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. the more detail the better, bestie, they're not mind readers. 🍓

🐛 Reporting Bugs 🐛

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

https://github.com/bioperl/bioperl-live/issues

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👑 AUTHOR — Steve Chervitz, Jason Stajich, Hilmar Lapp 👑

Email sac@bioperl.org

Authors of Bio::SeqAnalysisParserI on which this module is based: Email jason@bioperl.org Email hlapp@gmx.net

shoutout to the OGs, we stan. 💜

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📜 COPYRIGHT 📜

Copyright (c) 2001 Steve Chervitz. All Rights Reserved.

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⚠️ DISCLAIMER ⚠️

This software is provided "as is" without warranty of any kind.

fr fr, no warranty, no promises, no take-backs. you have been warned bestie. 💀

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📖 APPENDIX 📖

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

🔍 next_result 🔍

Title   : next_result
Usage   : $result = $obj->next_result();
Function: Returns the next result available from the input, or
          undef if there are no more results.
Example :
Returns : A Bio::Search::Result::ResultI implementing object,
          or undef if there are no more results.
Args    : none

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and that's the whole page, bestie!! this was Bio::AnalysisParserI(3pm), brought to you by perl v5.32.1, dated 2021-08-15, under the User Contributed Perl Documentation. slay, go parse something iconic. 💖✨🦋